Cryo-EM structure of human XKR8-basigin complex in lipid nanodisc
Resolution: 3.66 Å
EM Method: Single-particle
Fitted PDBs: 8xej
Q-score: 0.415
Sakuragi T, Kanai R, Otani M, Kikkawa M, Toyoshima C, Nagata S
J Biol Chem (2024) 300 pp. 105755-105755 [ Pubmed: 38364890 DOI: doi:10.1016/j.jbc.2024.105755 ]
- Human xkr8-basigin complex (Complex from Homo sapiens)
- Human xkr8-basigin complex bound to fab fragment in lipid nanodisc (110 kDa, Complex)
- 1,2-dilinoleoyl-sn-glycero-3-phosphocholine (782 Da, Ligand)
- Fab light chain (23 kDa, Protein from Oryctolagus cuniculus)
- Fab fragment (Complex from Oryctolagus cuniculus)
- Fab heavy chain (22 kDa, Protein from Oryctolagus cuniculus)
- Xk-related protein 8 (45 kDa, Protein from Homo sapiens)
- Isoform 2 of basigin (19 kDa, Protein from Homo sapiens)
Cryo-EM structure of human XKR8-basigin complex bound to Fab fragment
Resolution: 3.8 Å
EM Method: Single-particle
Fitted PDBs: 7dce
Q-score: 0.423
Sakuragi T, Kanai R, Tsutsumi A, Narita H, Onishi E, Nishino K, Miyazaki T, Baba T, Kosako H, Nakagawa A, Kikkawa M, Toyoshima C, Nagata S
Nat Struct Mol Biol (2021) 28 pp. 825-834 [ Pubmed: 34625749 DOI: doi:10.1038/s41594-021-00665-8 ]
- Human xkr8-basigin complex (Complex from Homo sapiens)
- 1,2-dilinoleoyl-sn-glycero-3-phosphocholine (782 Da, Ligand)
- Light chain of fab fragment (23 kDa, Protein from Oryctolagus cuniculus)
- Fab fragment (Complex from Oryctolagus cuniculus)
- Human xkr8-basigin complex bound to fab fragment (110 kDa, Complex)
- Heavy chain of fab fragment (22 kDa, Protein from Oryctolagus cuniculus)
- Xk-related protein 8 (45 kDa, Protein from Homo sapiens)
- Isoform 2 of basigin (19 kDa, Protein from Homo sapiens)
Cryo-EM structure of a human ATP11C-CDC50A flippase in E1-AMPPCP state
Resolution: 4.0 Å
EM Method: Single-particle
Fitted PDBs: 7bsp
Q-score: 0.477
Nakanishi H, Nishizawa T, Segawa K, Nureki O, Fujiyoshi Y, Nagata S, Abe K
Cell Rep (2020) 32 pp. 108208-108208 [ Pubmed: 32997992 DOI: doi:10.1016/j.celrep.2020.108208 ]
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Cdc50a (40 kDa, Protein from Homo sapiens)
- Atp11c (124 kDa, Protein from Homo sapiens)
- Human atp11c-cdc50a flippase (180 kDa, Complex from Homo sapiens)
- Phosphomethylphosphonic acid adenylate ester (505 Da, Ligand)
Cryo-EM structure of a human ATP11C-CDC50A flippase in E1AlF-ADP state
Resolution: 3.2 Å
EM Method: Single-particle
Fitted PDBs: 7bsq
Q-score: 0.567
Nakanishi H, Nishizawa T, Segawa K, Nureki O, Fujiyoshi Y, Nagata S, Abe K
Cell Rep (2020) 32 pp. 108208-108208 [ Pubmed: 32997992 DOI: doi:10.1016/j.celrep.2020.108208 ]
- Adenosine-5'-diphosphate (427 Da, Ligand)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Cdc50a (40 kDa, Protein from Homo sapiens)
- Atp11c (124 kDa, Protein from Homo sapiens)
- Human atp11c-cdc50a flippase (180 kDa, Complex from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- Tetrafluoroaluminate ion (102 Da, Ligand)
Cryo-EM structure of a human ATP11C-CDC50A flippase in E1AlF state
Resolution: 3.3 Å
EM Method: Single-particle
Fitted PDBs: 7bss
Q-score: 0.539
Nakanishi H, Nishizawa T, Segawa K, Nureki O, Fujiyoshi Y, Nagata S, Abe K
Cell Rep (2020) 32 pp. 108208-108208 [ Pubmed: 32997992 DOI: doi:10.1016/j.celrep.2020.108208 ]
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Cdc50a (40 kDa, Protein from Homo sapiens)
- Alpha-d-mannopyranose (180 Da, Ligand)
- Atp11c (124 kDa, Protein from Homo sapiens)
- Human atp11c-cdc50a flippase (180 kDa, Complex from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- Tetrafluoroaluminate ion (102 Da, Ligand)
Cryo-EM structure of a human ATP11C-CDC50A flippase in PtdSer-bound E2BeF state
Resolution: 3.2 Å
EM Method: Single-particle
Fitted PDBs: 7bsu
Q-score: 0.572
Nakanishi H, Nishizawa T, Segawa K, Nureki O, Fujiyoshi Y, Nagata S, Abe K
Cell Rep (2020) 32 pp. 108208-108208 [ Pubmed: 32997992 DOI: doi:10.1016/j.celrep.2020.108208 ]
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- O-[(r)-{[(2r)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-l-serine (792 Da, Ligand)
- Human atp11c-cdc50a flippase (180 kDa, Complex from Homo sapiens)
- Cell cycle control protein 50a (40 kDa, Protein from Homo sapiens)
- Atp11c (124 kDa, Protein from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- 1-deoxy-alpha-d-mannopyranose (164 Da, Ligand)
Cryo-EM structure of a human ATP11C-CDC50A flippase in PtdSer-occluded E2-AlF state
Resolution: 3.0 Å
EM Method: Single-particle
Fitted PDBs: 7bsv
Q-score: 0.585
Nakanishi H, Nishizawa T, Segawa K, Nureki O, Fujiyoshi Y, Nagata S, Abe K
Cell Rep (2020) 32 pp. 108208-108208 [ Pubmed: 32997992 DOI: doi:10.1016/j.celrep.2020.108208 ]
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Cdc50a (40 kDa, Protein from Homo sapiens)
- Atp11c (124 kDa, Protein from Homo sapiens)
- O-[(r)-{[(2r)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-l-serine (792 Da, Ligand)
- Human atp11c-cdc50a flippase (180 kDa, Complex from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- Water (18 Da, Ligand)
- Tetrafluoroaluminate ion (102 Da, Ligand)
Cryo-EM structure of a human ATP11C-CDC50A flippase in PtdEtn-occluded E2-AlF state
Resolution: 3.9 Å
EM Method: Single-particle
Fitted PDBs: 7bsw
Q-score: 0.475
Nakanishi H, Nishizawa T, Segawa K, Nureki O, Fujiyoshi Y, Nagata S, Abe K
Cell Rep (2020) 32 pp. 108208-108208 [ Pubmed: 32997992 DOI: doi:10.1016/j.celrep.2020.108208 ]
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Cdc50a (40 kDa, Protein from Homo sapiens)
- Alpha-d-mannopyranose (180 Da, Ligand)
- Atp11c (124 kDa, Protein from Homo sapiens)
- Human atp11c-cdc50a flippase (180 kDa, Complex from Homo sapiens)
- 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine (749 Da, Ligand)
- Tetrafluoroaluminate ion (102 Da, Ligand)